Coral reefs around the world are facing unprecedented rates of decline, resulting in a paradigm shift towards actively managing these ecosystems for resilience in the face of a rapidly changing climate. Fundamental to this is a detailed understanding of the spatial patterns and genetic mechanisms of bleaching resistance in reef coral. Genome-wide association studies (GWAS) represent a powerful means of unravelling the genetic correlates of bleaching resistance, particularly when combined with experimental set-ups that can reliably measure the bleaching response. In this study, we took our portable, state-of-the-art, coral stress tank system ('Sea-Sim-in-a-Box') to the remote Scott Reef in northwest Australia and carried out a series of acute heat stress experiments, and then coupled these data with high-coverage whole genome re-sequencing to identify any genetic correlates of bleaching. Our data revealed wide variation in bleaching response across the reef system and offer new insight into the genetic mechanisms underpinning this important climate-related trait.